When I loaded my level to work on it today, the lakes have stopped having water and no longer affect the landscape. I have the checkmark set to affect landscape and have layers set to editable on the landscape itself. Other levels have working rivers and lakes. Any help would be much appreciated.
I found the problem, the lakes were set to static. When I changed them to moveable it fixed them, hopefully this helps others.
Nice! For me all my rivers disappeared but this fixed it